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Merkel cell carcinoma (MCC) is a rare primary cutaneous neuroendocrine carcinoma. It occurs predominantly in the head and neck area and often behaves aggressively. In this single-institution retrospective observational cohort study, we describe the results of a treatment strategy that we developed over the past decades. Endpoints of this study were local, regional and distant control, disease-specific survival and overall survival. In total 47 patients with head and neck MCC, diagnosed in the Netherlands Cancer Institute-Antoni van Leeuwenhoek (NKI-AvL) between 1984 and 2012, were included in this study. Local tumor control was 82 % (95 % CI 71-95 %) at 5 years. Regional lymph node metastases were found at the moment of diagnosis in 13 cases (28 %). In the group of patients who were initially cN0, the 5-year regional control was 80 % (68-95 %). The 5-year metastasis-free interval probability was 80 % (68-94 %). The disease-specific survival (DSS) at 5 years was 70 % (56-86 %). An overall survival of 54 % (40-72 %) was found at 5-year follow-up and of 37 % (23-59 %) at 10-year follow-up. Univariable Cox regression analysis of many clinical and pathological variables did not identify any predictors for DSS. The MCC has a high propensity for locoregional and distant spread in the head and neck region. Undertreatment, especially of the lymph nodes in the neck, is a serious problem as regional (micro)metastasis are common even in T1 tumors. Future research will have to elucidate the role of the sentinel lymph node procedure versus the elective selective node dissection and standardized elective local and regional radiotherapy in the head and neck area.